/* --------------------------------------------------------------------- */
/*                                                                       */
/*           BAYESIAN MULTIMAPPER / INBRED LINE CROSSES  Version 1.0     */
/*                                                                       */
/*           (c) Copyright 1996-2006 by Mikko J. Sillanpaa               */
/*                                                                       */
/*            Rolf Nevanlinna Institute                                  */
/*            FIN-00014 University of Helsinki, FINLAND                  */
/*                                                                       */
/*            E-mail : mjs@rolf.helsinki.fi                              */
/*                                                                       */
/*                  last updated : February 2002                         */
/*                                                                       */
/* --------------------------------------------------------------------- */
/* This file is part of the Multimapper software.                        */ 
/* The Multimapper software has been written only for scientific use.    */ 
/* There is absolutely no warranty in the Multimapper software.          */  
/* You are using the Multimapper software completely at your own risk.   */
/* Beware! this is the version 1.0, the Multimapper software might       */
/* contain some errors or bugs!                                          */
/*                                                                       */
/* --------------------------------------------------------------------- */
/*                                                                       */
/*   file name:         data_structure.h  (header file)                  */
/*                                                                       */
/*   main datastructures for whole program                               */
/*                                                                       */
/*                                                                       */
/* --------------------------------------------------------------------- */

#define MAX_N_CHROMOS 50      /* max number of chromosomes            */ 
#define MAX_N_MARKERS 50      /* max number of markers per chromosome */
#define MAX_N_BG_CONT 50      /* max number of background controls    */
#define MAX_N_GENOTYP 50      /* max number of genotypes              */ 
#define MAX_N_INDIVID 500     /* max number of individuals            */ 
#define MAX_N_QTL 3           /* max number of QTLs                   */
#define MAX_N_COV 10          /* max number of covariates             */
#define MAX_N_CLASSES 30      /* max number of classes in covariates  */


long lrand48(void);
#define rand() lrand48()
#undef RAND_MAX
#define RAND_MAX 2147483647


/* int Nind;       */             /* number of individuals */
/* int Ngen;       */             /* number of possible genotypes */
/* int N_bc;       */             /* number of background controls */
/* double *alpha;  */             /* vector (1..N_gen) of possible genotypes */
/* double *X;      */             /* (N_bc x Nind) matrix of bc genotypes */


typedef struct regression_parameters {
  double a;                              /* mean */
  double sigma;                          /* residual variance */
  double b[MAX_N_QTL][MAX_N_GENOTYP];    /* vector for genotypic coeff. */
  double bc[MAX_N_BG_CONT][MAX_N_GENOTYP]; /* matrix for bg. control coeff. */
  double cov[MAX_N_COV][MAX_N_CLASSES]; /* r-coeff/classification covar */
} regpa;

/* --------------------------------------------------------------------- */
/*    support structure for markers and their order and                  */ 
/*    recombination fractions between them                               */
/* --------------------------------------------------------------------- */ 

typedef struct mark { 
   int marker;         /* marker nro */
   char *name;         /* marker name */
   double r;           /* recomb. fract. between this and next marker */
   double dist;        /* same distance in centiMorgans */
   struct mark *next;  /* pointer to next marker */
 } markers;


typedef struct QTL {
  double l_x;       /* location of QTL   */
  int ML;           /* number-1 of left flanking marker */
  int MR;           /* number-1 of right flanking marker */
  markers *g_l;     /* pointer to left flanking marker */     
  markers *g_r;     /* pointer to right flanking marker */     /* not used */
  double r1;        /* recombination fraction between QTL and left fl. m. */
  double r2;        /* recombination fraction between QTL and right fl. m. */
} QTL_type;

typedef struct chromosome {
  int chromosome_number;    /* chromosome number */
  char *name;               /* chromosome name   */
  markers *start;           /* pointer to markers */
  struct chromosome *next;  /* pointer to next chromosome */
} chromosome_type;

/* --------------------------------------------------------------------- */

/* --------------------------------------------------------------------- */
/*    support structure for individuals phenotypes and                   */ 
/*    complete and incomplete genotypes                                  */
/* --------------------------------------------------------------------- */
typedef struct geno {
  int genotype;            /* coded individual genotype */
  chromosome_type *chr;    /* pointer telling which chromosome */
  markers *marker;         /* pointer telling which marker */
  struct geno *next;       /* pointer to next marker genotype */
} geno_type;

typedef struct ind {
  int number;                /* individual number */ 
  double phenotype[10];      /* phenotype of this individual */
  geno_type *start;          /* pointer to start of incomplete genotypes */
  struct ind *next;          /* pointer to next individual */
} individuals;

/* --------------------------------------------------------------------- */


/* following structure is not used in this implementation*/

typedef struct c_m {         
  int genotype;              /* coded individual genotype */
  geno_type *info;           /* pointer to location information */
  struct c_m *next;          /* pointer to next marker */
} complete_markers;